bob.bio.base issueshttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues2023-08-22T08:07:17Zhttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/194Loading scores for the measure commands fails on non-float scores2023-08-22T08:07:17ZYannick DAYERLoading scores for the measure commands fails on non-float scores[src/bob/bio/base/score/load.py#L663](https://gitlab.idiap.ch/bob/bob.bio.base/-/blob/master/src/bob/bio/base/score/load.py#L663) and [src/bob/bio/base/score/load.py#L650](https://gitlab.idiap.ch/bob/bob.bio.base/-/blob/master/src/bob/bi...[src/bob/bio/base/score/load.py#L663](https://gitlab.idiap.ch/bob/bob.bio.base/-/blob/master/src/bob/bio/base/score/load.py#L663) and [src/bob/bio/base/score/load.py#L650](https://gitlab.idiap.ch/bob/bob.bio.base/-/blob/master/src/bob/bio/base/score/load.py#L650) cast a CSV score column to float, but it could contain other things (nothing or `None`) that cannot be converted to float. This needs to be handled correctly.
Possible solution:
- Convert all non-float values to `float("nan")`, this should be handled correctly by the measure commands.https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/192vuln hist command missing far_value option2023-05-01T15:11:06ZAlain KOMATYvuln hist command missing far_value optionExecuting the command:
```
bob vuln hist -c far --far-value 0.001 scores-dev.csv --output 11_hist.pdf --figsize "6,5"
```
Outputs the following error:
```
Error: No such option: --far-value Did you mean --iapmr-line?
```Executing the command:
```
bob vuln hist -c far --far-value 0.001 scores-dev.csv --output 11_hist.pdf --figsize "6,5"
```
Outputs the following error:
```
Error: No such option: --far-value Did you mean --iapmr-line?
```https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/186Migrating the database interfaces to the new new CSV format2022-09-06T13:19:13ZAmir MOHAMMADIMigrating the database interfaces to the new new CSV formatA new interface is being implemented in https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/300, and I am trying to migrate all dbs to that.
This is a meta issue to track the migration.
- [ ] Convert all csv based ones to the new ...A new interface is being implemented in https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/300, and I am trying to migrate all dbs to that.
This is a meta issue to track the migration.
- [ ] Convert all csv based ones to the new format
- [ ] Convert all custom interfaces to the new format
- [ ] Rewrite `bob.bio.face.database` file for database that were using custom interface
- [ ] Test and verify the new interfaces!
- [ ] Upload csv files according to https://gitlab.idiap.ch/bob/private/-/wikis/How-to-upload-resources
- follow the `data/bob/bob.bio.modality/bio-modality-database_name.tar.gz`
- Use this format in the code:
```python
from bob.extension.download import get_file
name = "bio-modality-database_name-586b7e81.tar.gz"
dataset_protocols_path = get_file(
name,
# don't use https here, use http so the link works in the CI as well.
[f"https://www.idiap.ch/software/bob/data/bob/bob.bio.modality/{name}",
f"http://www.idiap.ch/software/bob/data/bob/bob.bio.modality/{name}"],
cache_subdir="protocols",
file_hash="586b7e81",
)
# remove .urls method.
```
Separate problems
- [ ] asvspoof2017-spoof the interface does not load
- [ ] utfvp has some columns without header in its CSV files!
- [ ] caspeal has some columns without header in its CSV files!
- [ ] gbu, rfw, lfw, ijbc, youtube interfaces are custom
- [ ] bob.bio.spear licit and spoof protocols need to change to new format like replaymobileLaurent COLBOISLaurent COLBOIShttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/181re-enable cllr tests2022-05-12T13:36:23ZAmir MOHAMMADIre-enable cllr testsafter https://gitlab.idiap.ch/bob/bob.measure/-/issues/67 is resolved
by reverting https://gitlab.idiap.ch/bob/bob.bio.base/-/commit/7bee57cbfd1e98b2bc4f6e0044eeb178fdf766b4after https://gitlab.idiap.ch/bob/bob.measure/-/issues/67 is resolved
by reverting https://gitlab.idiap.ch/bob/bob.bio.base/-/commit/7bee57cbfd1e98b2bc4f6e0044eeb178fdf766b4The Great Deprecationhttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/178It would be great if we could provide documentation here on how to enable/dis...2022-04-01T14:15:17ZTiago de Freitas PereiraIt would be great if we could provide documentation here on how to enable/disable the fit function from being calledThe following discussion from !280 should be addressed:
- [ ] @mguenther started a [discussion](https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/280#note_72711): (+1 comment)
> It would be great if we could provide docume...The following discussion from !280 should be addressed:
- [ ] @mguenther started a [discussion](https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/280#note_72711): (+1 comment)
> It would be great if we could provide documentation here on how to enable/disable the fit function from being called.Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/172There is no algorithm available to compute average features2021-12-15T14:41:32ZManuel Günthersiebenkopf@googlemail.comThere is no algorithm available to compute average featuresRelated to bob/bob.bio.face#73
The current best way of handling several deep features for enrollment or probing is to compute there average. Currently, this is not implemented. This issue is used to keep track of the implementation of t...Related to bob/bob.bio.face#73
The current best way of handling several deep features for enrollment or probing is to compute there average. Currently, this is not implemented. This issue is used to keep track of the implementation of that feature.Manuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/170We have no clear documentation on how to handle supervised training.....2022-04-25T17:38:13ZTiago de Freitas PereiraWe have no clear documentation on how to handle supervised training........ while using `vanilla-biometrics`.
Internally, we know that we need to add this kwarg to the transformer that does the fit `fit_extra_arguments = (("y", "subject_id"),)` linking the `subject_id` from the sample with the `y` parameter...... while using `vanilla-biometrics`.
Internally, we know that we need to add this kwarg to the transformer that does the fit `fit_extra_arguments = (("y", "subject_id"),)` linking the `subject_id` from the sample with the `y` parameter of the `BaseEstimator`.
However, this is obscure in the documentation.
We need a proper documentation and a simple example.Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/169CLI plotting commands inconsistent2021-12-15T15:13:31ZManuel Günthersiebenkopf@googlemail.comCLI plotting commands inconsistentWhen using the plotting commands for bob, some of the parameters are expected to be separated by space, and some by comma. For example, the following command does not work:
```
bob bio dir scores-1 scores-2 --legends label-1 label-2
```...When using the plotting commands for bob, some of the parameters are expected to be separated by space, and some by comma. For example, the following command does not work:
```
bob bio dir scores-1 scores-2 --legends label-1 label-2
```
This raises the error:
```
Usage: bob bio dir [OPTIONS] [SCORES]...
Try 'bob bio dir -?' for help.
Error: Invalid value: Number of legends must be >= to the number of systems
```
In fact, the score files must be separated by space, and the legends by comma, in order to work:
```
bob bio dir scores-1 scores-2 --legends label-1,label-2
```
Is there any particular reason for this behavior, i.e., is this expected?https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/165Move some features from bob.measure to bob.bio.base2021-11-26T17:45:12ZTiago de Freitas PereiraMove some features from bob.measure to bob.bio.baseAs we've discussed in the last bob meeting we decided to move some biometric specific features from `bob.measure` to `bob.bio.base`
The candidate features are the following (including the plot extension of it):
- bob.measure.cmc
- bo...As we've discussed in the last bob meeting we decided to move some biometric specific features from `bob.measure` to `bob.bio.base`
The candidate features are the following (including the plot extension of it):
- bob.measure.cmc
- bob.measure.dir
- bob.measure.epc
- ANYTHING ELSE?
Depends on: https://gitlab.idiap.ch/bob/bob.measure/-/merge_requests/103
ping @amohammadi @lcolbois @ydayer
Thankshttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/163`annotate` does not create files for empty annotations2021-11-24T10:07:55ZYannick DAYER`annotate` does not create files for empty annotationsMissing annotations files lead to errors when trying to load them later on.
Files are not created since we use `CheckpointWrapper` to save them and it skips samples with `output_attribute == None`.
Need to change the save system of [th...Missing annotations files lead to errors when trying to load them later on.
Files are not created since we use `CheckpointWrapper` to save them and it skips samples with `output_attribute == None`.
Need to change the save system of [the `annotate` script](https://gitlab.idiap.ch/bob/bob.bio.base/-/blob/master/bob/bio/base/script/annotate.py#L106) to not use `CheckpointWrapper`.
Expected behavior: Failed execution of the annotator on a sample still creates a file for that sample with `"null"` or another expected value.Yannick DAYERYannick DAYERhttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/162Follow-up from "Making Distance algorithm (enroll and scoring) more robust wh...2021-09-10T07:50:49ZTiago de Freitas PereiraFollow-up from "Making Distance algorithm (enroll and scoring) more robust while different..."Create a Wrapper on `bob.bio.base.pipelines.vanilla_biometrics.BioAlgorithm` to handle videos as input.
ping @mguenther @amohammadi
The following discussion from !264 should be addressed:
- [ ] @mguenther started a [discussion](https...Create a Wrapper on `bob.bio.base.pipelines.vanilla_biometrics.BioAlgorithm` to handle videos as input.
ping @mguenther @amohammadi
The following discussion from !264 should be addressed:
- [ ] @mguenther started a [discussion](https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/264#note_65532): (+4 comments)
> My idea was rather that the `bob.bio.video` Wrapper solves this issue by transforming the `Sample`s from a video into a `SampleSet`, but I am not sure how difficult that would be in the new version.https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/156`resources.py --details` does not work if database interface is not installed2021-06-16T13:54:51ZManuel Günthersiebenkopf@googlemail.com`resources.py --details` does not work if database interface is not installedWhen running `resources.py --types d --details`, the script fails with the following exception:
```
List of registered databases:
Traceback (most recent call last):
File "envs/bob-9/bin/resources.py", line 33, in <module>
sys.exit...When running `resources.py --types d --details`, the script fails with the following exception:
```
List of registered databases:
Traceback (most recent call last):
File "envs/bob-9/bin/resources.py", line 33, in <module>
sys.exit(load_entry_point('bob.bio.base==5.0.0', 'console_scripts', 'resources.py')())
File "envs/bob-9/lib/python3.8/site-packages/bob/bio/base/script/resources.py", line 32, in resources
print (bob.bio.base.list_resources('database', **kwargs))
File "/envs/bob-9/lib/python3.8/site-packages/bob/bio/base/utils/resources.py", line 315, in list_resources
retval += " ==> " + str(entry_point.load()) + "\n\n"
File "envs/bob-9/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2450, in load
return self.resolve()
File "envs/bob-9/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2456, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "envs/bob-9/lib/python3.8/site-packages/bob/bio/face/config/database/arface.py", line 10, in <module>
ARFaceBioDatabase(
File "envs/bob-9/lib/python3.8/site-packages/bob/bio/face/database/arface.py", line 36, in __init__
from bob.db.arface.query import Database as LowLevelDatabase
ModuleNotFoundError: No module named 'bob.db.arface'
```
Unfortunately, I cannot (easily) install the databases in python 3.8, see https://stackoverflow.com/questions/68003751/why-are-the-bob-databases-e-g-bob-db-arface-not-available-for-python-3-8
I think, there should a a `try/except` wrapper around loading the resources in detail mode, and only list those for which the databases are actually installed.https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/145It's not possible to provide a dask wrapped pipeline and a dask client2020-11-17T09:53:56ZAmir MOHAMMADIIt's not possible to provide a dask wrapped pipeline and a dask clientI want to use custom dask tags and hence want to wrap the estimators myself in the config file.
but this is not possible as when I provide a dask client, the pipeline is again wrapped in dask.I want to use custom dask tags and hence want to wrap the estimators myself in the config file.
but this is not possible as when I provide a dask client, the pipeline is again wrapped in dask.Bob 9.0.0https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/139Protect against paths starting with / in database filelist API2020-10-16T15:58:14ZAmir MOHAMMADIProtect against paths starting with / in database filelist APIIf the paths in the filelists of the filelist-based db interfaces start with `/` and we are checkpointing samples, there is a good chance that original samples of the database could be re-written.
We should either check for this and rais...If the paths in the filelists of the filelist-based db interfaces start with `/` and we are checkpointing samples, there is a good chance that original samples of the database could be re-written.
We should either check for this and raise an error, or fix this automatically.Bob 9.0.0https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/136resources.py as CLI command2021-06-16T13:54:52ZTiago de Freitas Pereiraresources.py as CLI commandHi,
The `resources.py` is a very usesul script and we need to add it in our `bob bio` CLI "umbrella" .
Furthermore, we need to decide which type of resources should be kept and which should be dropped.
Today, the options available via ...Hi,
The `resources.py` is a very usesul script and we need to add it in our `bob bio` CLI "umbrella" .
Furthermore, we need to decide which type of resources should be kept and which should be dropped.
Today, the options available via `-t` are:
- d,database,
- p,preprocessor,
- e,extractor,
- a,algorithm,
- g,grid,
- c,config,
- an,annotator,
- b,baseline
I think now we should have something like:
- d,database,
- t,transformer,
- a,biometric_algorithm,
- d,dask_client,
- c,config,
- an,annotator,
- b,baseline
ping @ydayerBob 9.0.0https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/124CMC and ROC curves with error bars (confidence intervals)2018-06-27T13:55:18ZAmir MOHAMMADICMC and ROC curves with error bars (confidence intervals)As requested in bob.measure#38, here is an example figure:
[ISV_gaussians.pdf](/uploads/c65eb7d031fb0e6012fc65d3333b9781/ISV_gaussians.pdf)
I just have another point that these error bars should be confidence intervals not stds.
We have...As requested in bob.measure#38, here is an example figure:
[ISV_gaussians.pdf](/uploads/c65eb7d031fb0e6012fc65d3333b9781/ISV_gaussians.pdf)
I just have another point that these error bars should be confidence intervals not stds.
We have a confidence interval function in bob.measure.Tiago de Freitas PereiraTiago de Freitas Pereira